Single Jenkins instance using multiple Sonar instances

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Is it possible to configure Jenkins to use multiple Sonar instances?

Currently we are using one Sonar instance for legacy projects (Java 6) and a new Sonar instance for Java 8

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Yes, in Manage Jenkins > Configure System you can add as many Sonarqube installations as you want in the Sonar section. Then when you configure a job to perform the Sonar analysis you can select what instance you want to use from a drop down list.